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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.
Term:Encephalocele
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Accession:DOID:9000983 term browser browse the term
Definition:Brain tissue herniation through a congenital or acquired defect in the skull. The majority of congenital encephaloceles occur in the occipital or frontal regions. Clinical features include a protuberant mass that may be pulsatile. The quantity and location of protruding neural tissue determines the type and degree of neurologic deficit. Visual defects, psychomotor developmental delay, and persistent motor deficits frequently occur.
Synonyms:exact_synonym: Acquired Encephalocele;   Acquired Encephaloceles;   Bifid Cranium;   Bifid Craniums;   Cephalocele;   Cephaloceles;   Cerebellar Hernia;   Cerebellar Hernias;   Cerebellar Herniation;   Cerebellar Herniations;   Cerebral Hernia;   Cerebral Hernias;   Cranial Meningoencephalocele;   Cranial Meningoencephaloceles;   Craniocele;   Cranioceles;   Cranium Bifidum;   Cranium Bifidums;   Encephaloceles;   Frontal Encephalocele;   Frontal Encephaloceles;   Notoencephalocele;   Notoencephaloceles;   Occipital Encephalocele;   Occipital Encephaloceles;   Sincipital Encephalocele;   Sincipital Encephaloceles;   Tonsillar Hernia;   Tonsillar Hernias;   Tonsillar Herniation;   Tonsillar Herniations
 primary_id: MESH:D004677;   RDO:0001577
For additional species annotation, visit the Alliance of Genome Resources.


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Encephalocele term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cc2d2a coiled-coil and C2 domain containing 2A ISO ClinVar Annotator: match by term: Encephalocele ClinVar PMID:19777577 PMID:25741868 PMID:26862157 PMID:28492532 PMID:31680349 NCBI chr14:67,349,004...67,435,883
Ensembl chr14:67,351,353...67,435,949 		JBrowse link
G Cep290 centrosomal protein 290 ISO ClinVar Annotator: match by term: Encephalocele | ClinVar Annotator: match by term: Occipital encephalocele ClinVar PMID:16909394 PMID:17345604 PMID:17564974 PMID:17705300 PMID:20683928 More... NCBI chr 7:35,310,071...35,399,392
Ensembl chr 7:35,310,199...35,399,392 		JBrowse link
G Dnai3 dynein axonemal intermediate chain 3 ISO ClinVar Annotator: match by term: Occipital encephalocele ClinVar PMID:29285825 NCBI chr 2:234,947,910...235,006,173
Ensembl chr 2:234,929,677...235,006,173 		JBrowse link
G Pibf1 progesterone immunomodulatory binding factor 1 ISO ClinVar Annotator: match by term: Cephalocele ClinVar PMID:25741868 PMID:26167768 PMID:30858804 PMID:31474318 NCBI chr15:75,850,389...76,019,711
Ensembl chr15:75,850,624...76,019,712 		JBrowse link
G Rpgrip1l Rpgrip1-like ISO associated with Meckel Syndrome, Type 5;DNA:mutations:exons: RGD PMID:17558409 RGD:11073359 NCBI chr19:15,692,189...15,785,083
Ensembl chr19:15,692,150...15,785,083 		JBrowse link
G Szt2 SZT2 subunit of KICSTOR complex ISO ClinVar Annotator: match by term: Encephalocele ClinVar PMID:23932106 PMID:25741868 PMID:28492532 PMID:31680349 NCBI chr 5:131,897,250...131,943,953
Ensembl chr 5:131,897,275...131,943,904 		JBrowse link
Knobloch Syndrome term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adamts18 ADAM metallopeptidase with thrombospondin type 1 motif, 18 ISO ClinVar Annotator: match by term: Knobloch syndrome ClinVar PMID:21862674 PMID:23667181 PMID:28492532 NCBI chr19:41,686,951...41,840,035
Ensembl chr19:41,688,617...41,839,781 		JBrowse link
G Col18a1 collagen type XVIII alpha 1 chain ISO ClinVar Annotator: match by term: Knobloch syndrome OMIM
ClinVar		 PMID:1554013 PMID:9536098 PMID:10942434 PMID:12415512 PMID:14695535 More... NCBI chr20:11,474,104...11,582,593
Ensembl chr20:11,474,104...11,582,593 		JBrowse link
G Slc19a1 solute carrier family 19 member 1 ISO ClinVar Annotator: match by term: Knobloch syndrome ClinVar PMID:1554013 PMID:9536098 PMID:12415512 PMID:14695535 PMID:17546652 More... NCBI chr20:11,584,410...11,602,429
Ensembl chr20:11,584,411...11,601,972 		JBrowse link
Meckel syndrome 1 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cc2d2a coiled-coil and C2 domain containing 2A ISO ClinVar Annotator: match by term: DYSENCEPHALIA SPLANCHNOCYSTICA | ClinVar Annotator: match by term: Dysencephalia splachnocystica | ClinVar Annotator: match by term: Gruber syndrome ClinVar PMID:16199547 PMID:18950740 PMID:19777577 PMID:22241855 PMID:22425360 More... NCBI chr14:67,349,004...67,435,883
Ensembl chr14:67,351,353...67,435,949 		JBrowse link
G Cep290 centrosomal protein 290 ISO ClinVar Annotator: match by term: DYSENCEPHALIA SPLANCHNOCYSTICA | ClinVar Annotator: match by term: Dysencephalia splachnocystica ClinVar PMID:16199547 PMID:16909394 PMID:17345604 PMID:17409309 PMID:17564967 More... NCBI chr 7:35,310,071...35,399,392
Ensembl chr 7:35,310,199...35,399,392 		JBrowse link
G Fto FTO, alpha-ketoglutarate dependent dioxygenase ISO ClinVar Annotator: match by term: Dysencephalia splachnocystica ClinVar PMID:28492532 NCBI chr19:15,284,898...15,692,142
Ensembl chr19:15,349,696...15,692,083 		JBrowse link
G LOC120095383 U8 small nucleolar RNA ISO ClinVar Annotator: match by term: Meckel syndrome, type 1 ClinVar PMID:25741868 PMID:27571260 NCBI chr10:53,774,811...53,774,946
Ensembl chr10:53,774,811...53,774,946 		JBrowse link
G Mks1 MKS transition zone complex subunit 1 ISO ClinVar Annotator: match by term: Dysencephalia splachnocystica | ClinVar Annotator: match by term: Meckel syndrome, type 1
DNA:splice-site mutations:intron:c.870-2A>G, c.1546+1G¿¿¿>A (human)
DNA:deletion:intron:IVS15-7_35del (human)
DNA:splice-site mutation:intron:c.515 + 6T>C (mouse)
DNA:missense mutations, splice-site mutations:exon:c.417G>A, c.958G>A (p.V320I), c.1490G>A (p.R497K) (human)		 OMIM
ClinVar
RGD		 PMID:9536098 PMID:16199547 PMID:16415886 PMID:17185389 PMID:17377820 More... RGD:11535078, RGD:11535074, RGD:11535068, RGD:11535065, RGD:11063991 NCBI chr10:72,655,921...72,667,007
Ensembl chr10:72,655,921...72,666,655 		JBrowse link
G Rpgrip1l Rpgrip1-like ISO ClinVar Annotator: match by term: DYSENCEPHALIA SPLANCHNOCYSTICA | ClinVar Annotator: match by term: Dysencephalia splachnocystica | ClinVar Annotator: match by term: Gruber syndrome ClinVar PMID:17558407 PMID:17558409 PMID:19430481 PMID:20301500 PMID:21866095 More... NCBI chr19:15,692,189...15,785,083
Ensembl chr19:15,692,150...15,785,083 		JBrowse link
G Tmem107 transmembrane protein 107 ISO ClinVar Annotator: match by term: Meckel syndrome, type 1 ClinVar PMID:25741868 PMID:27571260 NCBI chr10:53,772,153...53,774,685
Ensembl chr10:53,771,784...53,774,676 		JBrowse link
G Tmem67 transmembrane protein 67 ISO ClinVar Annotator: match by term: Dysencephalia splachnocystica | ClinVar Annotator: match by term: Gruber syndrome ClinVar PMID:9375913 PMID:17377820 PMID:17397051 PMID:18414213 PMID:19058225 More... NCBI chr 5:25,536,458...25,589,378
Ensembl chr 5:25,536,458...25,589,334 		JBrowse link
Meckel Syndrome 12 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Kif14 kinesin family member 14 ISO ClinVar Annotator: match by term: Meckel syndrome 12 OMIM
ClinVar		 PMID:24128419 PMID:25741868 PMID:28492532 NCBI chr13:47,926,975...47,990,598
Ensembl chr13:47,927,044...47,989,164 		JBrowse link
Meckel syndrome 13 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmem107 transmembrane protein 107 ISO ClinVar Annotator: match by term: Meckel syndrome 13 OMIM
ClinVar		 PMID:25741868 PMID:26123494 PMID:26595381 NCBI chr10:53,772,153...53,774,685
Ensembl chr10:53,771,784...53,774,676 		JBrowse link
Meckel syndrome 2 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmem216 transmembrane protein 216 ISO ClinVar Annotator: match by term: Meckel syndrome, type 2
DNA:missense,frameshift,nonsense mutations:cds,splice junction:		 OMIM
ClinVar
RGD		 PMID:16199547 PMID:18414213 PMID:20036350 PMID:20301500 PMID:20512146 More... RGD:11067331 NCBI chr 1:207,196,454...207,201,704
Ensembl chr 1:207,196,454...207,201,754 		JBrowse link
Meckel syndrome 3 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmem67 transmembrane protein 67 ISO
IAGP		 ClinVar Annotator: match by term: MECKEL-GRUBER SYNDROME, TYPE 3 | ClinVar Annotator: match by term: Meckel syndrome, type 3
DNA:deletion
DNA:deletions, missense mutation, splice-site mutations: :multiple
DNA:missense mutation:exon:p.P394L (rat)
DNA:missense mutation:exon:p.R549C (c.1645C>T) (human)
DNA:missense mutations: :p.M252T (c.755T>C), p.R441C (c.1392C>T) (human)
DNA:missense mutations:exon: p.M252T (755T>C), p.R440Q (1319G>A), p.L966P (2897T>C) (human)
DNA:missense mutations, splice-site mutation:exon:multiple		 OMIM
ClinVar
RGD		 PMID:2929661 PMID:9375913 PMID:9536098 PMID:16199547 PMID:16415887 More... RGD:11535945, RGD:11535082, RGD:11535082, RGD:11535080, RGD:11535078, RGD:11068761, RGD:11063991 NCBI chr 5:25,536,458...25,589,378
Ensembl chr 5:25,536,458...25,589,334 		JBrowse link
G Tmem67wpk transmembrane protein 67; wpk mutant IAGP RGD PMID:16415887 RGD:11535082
Meckel syndrome 4 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cep290 centrosomal protein 290 ISO ClinVar Annotator: match by term: MECKEL-GRUBER SYNDROME, TYPE 4 | ClinVar Annotator: match by term: Meckel syndrome, type 4
DNA:frameshift mutation:exon:c.5489del (human)		 OMIM
ClinVar
RGD		 PMID:9536098 PMID:16199547 PMID:16682970 PMID:16682973 PMID:16909394 More... RGD:11070805 NCBI chr 7:35,310,071...35,399,392
Ensembl chr 7:35,310,199...35,399,392 		JBrowse link
G RGD1307947 similar to RIKEN cDNA C430008C19 ISO ClinVar Annotator: match by term: Meckel syndrome, type 4 ClinVar PMID:28492532 NCBI chr 7:35,396,876...35,408,633
Ensembl chr 7:35,397,995...35,409,600 		JBrowse link
G Tmem218 transmembrane protein 218 ISO ClinVar Annotator: match by term: Meckel syndrome, type 4 ClinVar PMID:33791682 NCBI chr 8:36,924,553...36,940,564
Ensembl chr 8:36,924,585...36,939,927 		JBrowse link
Meckel syndrome 5 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rpgrip1l Rpgrip1-like ISO ClinVar Annotator: match by term: Meckel syndrome, type 5 OMIM
ClinVar		 PMID:17558407 PMID:17558409 PMID:18414213 PMID:19430481 PMID:20301500 More... NCBI chr19:15,692,189...15,785,083
Ensembl chr19:15,692,150...15,785,083 		JBrowse link
Meckel syndrome 6 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cc2d2a coiled-coil and C2 domain containing 2A ISO ClinVar Annotator: match by term: Meckel syndrome, type 6 OMIM
ClinVar		 PMID:8253763 PMID:9536098 PMID:16199547 PMID:17576681 PMID:18414213 More... NCBI chr14:67,349,004...67,435,883
Ensembl chr14:67,351,353...67,435,949 		JBrowse link
G Cep290 centrosomal protein 290 ISO ClinVar Annotator: match by term: Meckel syndrome, type 6 ClinVar PMID:16682970 PMID:16682973 PMID:16909394 PMID:17345604 PMID:17564967 More... NCBI chr 7:35,310,071...35,399,392
Ensembl chr 7:35,310,199...35,399,392 		JBrowse link
G Tctn2 tectonic family member 2 ISO ClinVar Annotator: match by term: Meckel syndrome, type 6 ClinVar PMID:21462283 PMID:23169490 PMID:26729329 NCBI chr12:31,982,440...32,007,242
Ensembl chr12:31,822,733...32,007,069 		JBrowse link
parietal foramina term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Alx4 ALX homeobox 4 ISO ClinVar Annotator: match by term: Enlarged parietal foramina
CTD Direct Evidence: marker/mechanism		 ClinVar
CTD		 PMID:11137991 NCBI chr 3:79,611,682...79,648,260
Ensembl chr 3:79,611,719...79,648,260 		JBrowse link
G Msx2 msh homeobox 2 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Enlarged parietal foramina		 CTD
ClinVar		 PMID:7597092 PMID:8106171 PMID:8357019 PMID:8968743 PMID:9256341 More... NCBI chr17:11,097,214...11,102,879
Ensembl chr17:11,097,103...11,102,879 		JBrowse link
Parietal Foramina 1 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Msx2 msh homeobox 2 ISO ClinVar Annotator: match by term: Parietal foramina 1 OMIM
ClinVar		 PMID:10742103 PMID:10767351 PMID:16222674 PMID:25741868 PMID:28492532 NCBI chr17:11,097,214...11,102,879
Ensembl chr17:11,097,103...11,102,879 		JBrowse link
Parietal Foramina 2 term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Alx4 ALX homeobox 4 ISO ClinVar Annotator: match by term: Parietal foramina 2 OMIM
ClinVar		 PMID:11106354 PMID:11137991 PMID:16319823 PMID:22829454 PMID:24764194 More... NCBI chr 3:79,611,682...79,648,260
Ensembl chr 3:79,611,719...79,648,260 		JBrowse link
Parietal Foramina with Cleidocranial Dysplasia term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Msx2 msh homeobox 2 ISO ClinVar Annotator: match by term: Parietal foramina with cleidocranial dysplasia OMIM
ClinVar		 PMID:14571277 NCBI chr17:11,097,214...11,102,879
Ensembl chr17:11,097,103...11,102,879 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18030
    physical disorder 4045
      neural tube defect 125
        Encephalocele 23
          Cerebellar Vermis Aplasia with Associated Features suggesting Smith-Lemli-Opitz Syndrome and Meckel Syndrome 0
          Cerebrorenodigital Syndrome with Limb Malformations and Triradiate Acetabula 0
          DK Phocomelia Syndrome 0
          Dandy-Walker Malformation with Occipital Cephalocele, Autosomal Dominant 0
          Fronto-Facio-Nasal Dysplasia 0
          Knobloch Syndrome 3
          Knobloch Syndrome Type II 0
          Knobloch Syndrome Type III 0
          Laryngeal Atresia, Encephalocele, and Limb Deformities 0
          Meckel Syndrome 12 1
          Meckel syndrome 1 8
          Meckel syndrome 13 1
          Meckel syndrome 2 1
          Meckel syndrome 3 3
          Meckel syndrome 4 3
          Meckel syndrome 5 1
          Meckel syndrome 6 3
          Meckel-Like Cerebrorenodigital Syndrome 0
          Podder-Tolmie Syndrome 0
          Sakoda Complex 0
          Zechi-Ceide Syndrome 0
          parietal foramina + 2
Path 2
Term Annotations click to browse term
  disease 18030
    disease of anatomical entity 17410
      Urogenital Diseases 4682
        Female Urogenital Diseases and Pregnancy Complications 2212
          Female Urogenital Diseases 1835
            female reproductive system disease 1831
              prolapse of female genital organ 188
                enterocele 188
                  Encephalocele 23
                    Cerebellar Vermis Aplasia with Associated Features suggesting Smith-Lemli-Opitz Syndrome and Meckel Syndrome 0
                    Cerebrorenodigital Syndrome with Limb Malformations and Triradiate Acetabula 0
                    DK Phocomelia Syndrome 0
                    Dandy-Walker Malformation with Occipital Cephalocele, Autosomal Dominant 0
                    Fronto-Facio-Nasal Dysplasia 0
                    Knobloch Syndrome 3
                    Knobloch Syndrome Type II 0
                    Knobloch Syndrome Type III 0
                    Laryngeal Atresia, Encephalocele, and Limb Deformities 0
                    Meckel Syndrome 12 1
                    Meckel syndrome 1 8
                    Meckel syndrome 13 1
                    Meckel syndrome 2 1
                    Meckel syndrome 3 3
                    Meckel syndrome 4 3
                    Meckel syndrome 5 1
                    Meckel syndrome 6 3
                    Meckel-Like Cerebrorenodigital Syndrome 0
                    Podder-Tolmie Syndrome 0
                    Sakoda Complex 0
                    Zechi-Ceide Syndrome 0
                    parietal foramina + 2
paths to the root